[gmx-users] hblife

[Erik Marklund]

afsaneh maleki skrev:
> thanks dear justin'
>
> it is right that the output of the analysis tools generally writes 
> axis labels and data set legends. in hblife.xyg  file is written that  
> x axis  label "Time (ps)" and the last time is written 14300.001 
> whereas my simulated time is 40000 ps not 143000.00 ps   
> i send you this file
I don't remember the details about the calculation of lifetimes, but I 
believe it's an estimate of how the half lifes of hydrogen bonds. You 
can also get this quantity, along with the kinetic constants and 
energies for hb breaking and frormation, using -ac. If I remember 
correctly, -ac uses a more reliable method.

Erik
>
> Best wishes,
> Afsaneh
>
> On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     afsaneh maleki wrote:
>
>         Hi,
>
>         would you please elaborate the first column in the  hblife.xvg
>         file?
>         hblife.xyg is the output of the following command:
>         g_hbond -life hblife.xvg
>         this column don't show the real time in simulated system.what
>         are these times?
>
>
>     Check the headers in the .xvg file; the output of the analysis
>     tools generally writes axis labels and data set legends.  If it
>     still doesn't make sense, post a snippet of your file.
>
>     -Justin
>
>         thanks in advance,
>         Afsaneh
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys